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Related Concept Videos

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: Jul 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

Bernd W Brandt1, Jaap Heringa, Jack A M Leunissen

  • 1Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

Nucleic Acids Research
|May 9, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces SEQATOMS, a novel database for the Protein Data Bank (PDB). It masks missing protein residues, enabling sensitive similarity searches and better analysis of structural data.

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Last Updated: Jul 5, 2026

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) is a critical resource for macromolecular structures.
  • PDB files contain sequence and coordinate data, but some residues may be missing from coordinates, indicating unknown spatial positions.
  • Current similarity searches in PDB do not differentiate between residues with known and unknown 3D positions.

Purpose of the Study:

  • To develop a FASTA sequence database that integrates PDB sequence and coordinate information.
  • To enable case-sensitive BLAST searches that distinguish between known and unknown residue positions.
  • To facilitate the study of 'missing' regions in protein structures within their full sequence context.

Main Methods:

  • Created a FASTA sequence database by combining PDB sequence and coordinate information.
  • Masked residues absent from PDB coordinates using lower-case letters.
  • Developed a user-friendly BLAST interface for similarity searching with masked sequences.
  • Provided a masked version of the CATH domain database.

Main Results:

  • The SEQATOMS database effectively visualizes missing residues in their sequence context.
  • The BLAST interface allows for case-sensitive searches, preserving information about masked regions.
  • This approach aids in the investigation of unobserved regions in protein structures.

Conclusions:

  • SEQATOMS provides a valuable tool for analyzing protein structures with missing regions.
  • Case-sensitive BLAST searching with masked sequences enhances structural bioinformatics analysis.
  • The tool is publicly available at http://www.bioinformatics.nl/tools/seqatoms/.